GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf1N1B4_1379 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1379
          Length = 290

 Score =  216 bits (549), Expect = 6e-61
 Identities = 120/282 (42%), Positives = 166/282 (58%), Gaps = 31/282 (10%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           +EVVL V  +   FGG++ALSDV + +KR  ++ LIGPNGAGKTT FN +TG Y    G 
Sbjct: 2   SEVVLSVDKLMMHFGGIKALSDVSLKVKRNSIFALIGPNGAGKTTVFNCLTGFYKASGGH 61

Query: 66  FEL------------AGKPYEPT------------------AVHEVAKAGIARTFQNIRL 95
            EL             G+P++                      H + +AG+ARTFQNIRL
Sbjct: 62  IELNTRGVKTDVIKMLGEPFKAVDFVSPKSFINRLRYKMFGGTHLINRAGLARTFQNIRL 121

Query: 96  FAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKA 155
           F EM+ LEN++V +H+    G+   +  TKG++  E+     A   L+ V +   A+  A
Sbjct: 122 FREMSVLENLLVAQHMWVNRGMLAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRLA 181

Query: 156 RTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLRELIDRIRND-NRTILLIE 214
             LSYG QRRLEIARA+ T PQ+I LDEPAAG+N  E   L  +I  +R++ + T++LIE
Sbjct: 182 GELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLIE 241

Query: 215 HDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEAYLG 256
           HD+ +VM + D + VLD+G  IAEG P  ++ + KVI AYLG
Sbjct: 242 HDMGMVMSISDHIVVLDHGVVIAEGGPEAIRHDPKVIAAYLG 283


Lambda     K      H
   0.319    0.137    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 216
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 290
Length adjustment: 25
Effective length of query: 235
Effective length of database: 265
Effective search space:    62275
Effective search space used:    62275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory